added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / rarefactcommand.h

diff --git a/rarefactcommand.h b/rarefactcommand.h
index b4bce3e172d141ab5e1fdcea1c59bd35b25dadab..0e77a277e6ad7cda962a4c9476945f6b2aa6b557 100644 (file)
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -42,7 +42,7 @@ private:
        int nIters, abund, processors;
        float freq;
        
-       bool abort, allLines;
+       bool abort, allLines, groupMode;
        set<string> labels; //holds labels to be used
        string label, calc, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
        vector<string>  Estimators;
@@ -50,7 +50,8 @@ private:
        vector<string> groups;
        string outputDir;
        
-       vector<string> parseSharedFile(string);
+       vector<string> parseSharedFile(string, map<string, set<int> >&);
+       vector<string> createGroupFile(vector<string>&, map<int, string>);
 };
 
 #endif